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Databases used by the ASCC pipeline

This document describes the databases used by the pipeline.

nt Kraken

For building the database, install Kraken2 if it is not already installed. It can be installed using conda with this command:

conda install bioconda::kraken2

Commands for building the Kraken database:

kraken2-build --threads 16 --download-taxonomy --db nt
kraken2-build --threads 16 --download-library nt --db nt
kraken2-build --build --threads 16 --db nt

Warning: building this database requires hundreds of gigabytes of memory. See their Manual at: https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown

BUSCO5 database

Download from from: https://busco-data.ezlab.org/v5/data/.

NCBI taxdump, NCBI nt database and Uniprot Diamond database

Download and set up according to the instructions at https://blobtoolkit.genomehubs.org/install/.

Important Note: The NCBI nt BLAST database must have built-in taxonomy for the pipeline to work correctly. When building the BLAST database, make sure to include taxonomy information using the -parse_seqids and -taxid_map options with makeblastdb. Alternatively, you can download the pre-built BLAST database from NCBI which already includes taxonomy information.

NCBI nr Diamond database

Download the nr database protein FASTA files from the NCBI ftp server (wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz) and build the database similarly to the Uniprot Diamond database, following the instructions at https://blobtoolkit.genomehubs.org/install/.

FCS-GX database

Downloading instructions are at https://github.com/ncbi/fcs/wiki/FCS-GX-quickstart#download-the-fcs-gx-database.

FCS-adaptor

The FCS-adaptor database is included in the FCS-adaptor installation, so it doesn't need to be downloaded separately.

VecScreen

A FASTA file with the sequences for making a VecScreen database is included in the ASCC repository. It is the vecscreen_adaptors_for_screening_euks.fa file in the assets directory of this pipeline (vecscreen_adaptors_for_screening_euks.fa).

VecScreen requires a BLAST V4 database as input, we can generate this with the above file use the following.

makeblastdb -in vecscreen_adaptors_for_screening_euks.fa -parse_seqids -blastdb_version 4 -dbtype nucl

To use this database, point the vecscreen_database_path variable in the input YAML file of the pipeline run to the directory that contains this BLAST database. Use the name of the directory for vecscreen_database_path, without using the name of the database files. E.g. /path/to/my/database/files/vecscreen_database/.

PacBio barcodes

A FASTA file with the sequences of PacBio multiplexing barcodes is included in the ASCC repository. It is the pacbio_adaptors.fa file in the assets directory of this pipeline (pacbio_adaptors.fa).